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Jupyter widgets to visualize images in 2D and 3D

Project description

itk-jupyter-widgets
===================

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:target: https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/LICENSE
:alt: License

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:target: https://pypi.python.org/pypi/itkwidgets
:alt: PyPI

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:target: https://circleci.com/gh/InsightSoftwareConsortium/itk-jupyter-widgets
:alt: Build status

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:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb

Interactive `Jupyter <https://jupyter.org/>`_ widgets to visualize images in 2D and 3D.

.. image:: https://i.imgur.com/ERK5JtT.png
:width: 800px
:alt: Monkey brain volume rendering

These widgets are designed to support image analysis with the `Insight Toolkit
(ITK) <https://itk.org/>`_, but they also work with other spatial analysis tools
in the scientific Python ecosystem.

These widgets are built on
`itk.js <https://github.com/InsightSoftwareConsortium/itk-js>`_ and
`vtk.js <https://github.com/Kitware/vtk-js>`_.

.. image:: https://thumbs.gfycat.com/ShyFelineBeetle-size_restricted.gif
:width: 640px
:alt: itk-jupyter-widgets demo
:align: center

Installation
------------

To install, use pip::

pip install itkwidgets

Examples
--------

After installation, try the following examples that demonstrate how to visualize:

- `2D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/2DImage.ipynb>`_
- `3D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/3DImage.ipynb>`_
- `Dask Array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/DaskArray.ipynb>`_
- `ImageJ ImgLib2 images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/ImageJImgLib2.ipynb>`_ (requires `conda <https://conda.io/>`_ and a local `Fiji <https://fiji.sc/>`_ installation)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/scikit-image.ipynb>`_ (processed with scikit-image)
- `VTK vtkImageData <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/vtkImageData.ipynb>`_

Examples on Binder
--------

- `2D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F2DImage.ipynb>`_
- `3D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb>`_
- `Dask Array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/DaskArray.ipynb>`_
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/scikit-image.ipynb>`_ (processed with scikit-image)

Troubleshooting
---------------

If you experience the notebook warning::

IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.

Set the notebook configuration value::

jupyter notebook --NotebookApp.iopub_data_rate_limit=1e12

Hacking
-------

For a development installation (requires `Node.js <https://nodejs.org/en/download/>`_)::

git clone https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets.git
cd itk-jupyter-widgets
python -m pip install -r requirements-dev.txt -r requirements.txt
python -m pip install -e .
jupyter nbextension install --py --symlink --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix widgetsnbextension
python -m pytest

.. warning::

This project is under active development. Its API and behavior may change at
any time. We mean it.


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